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- PDB-3ek2: Crystal structure of eonyl-(acyl carrier protein) reductase from ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ek2 | ||||||
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Title | Crystal structure of eonyl-(acyl carrier protein) reductase from burkholderia pseudomallei 1719b | ||||||
![]() | Enoyl-(Acyl-carrier-protein) reductase (NADH) | ||||||
![]() | OXIDOREDUCTASE / SSGCID / enoyl-(acyl carrier protein) reductase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease | ||||||
Function / homology | ![]() enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid biosynthetic process / nucleotide binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
![]() | ![]() Title: Combining functional and structural genomics to sample the essential Burkholderia structome. Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 211.2 KB | Display | ![]() |
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PDB format | ![]() | 166.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3d63C ![]() 3dahC ![]() 3eizC ![]() 3ej2C ![]() 3ezoC ![]() 3f0fC ![]() 3ftpC ![]() 3gk0C ![]() 3gk3C ![]() 3gvfC ![]() 3gwaC ![]() 3gweC ![]() 3imlC ![]() 3sz8C ![]() 3t4cC ![]() 3tmlC ![]() 3tmqC ![]() 3txyC ![]() 3u7jC ![]() 3ue9C ![]() 3uk1C ![]() 3uk2C ![]() 3undC ![]() 3uptC ![]() 3urrC ![]() 3uw1C ![]() 3uw2C ![]() 3uw3C ![]() 3v2iC ![]() 3v7nC ![]() 3v8hC ![]() 3v9oC ![]() 3v9pC ![]() 3vavC ![]() 4ddoC ![]() 4dfeC ![]() 4dheC ![]() 4dhkC ![]() 4dutC ![]() 4dz4C ![]() 4e4tC ![]() 4efiC ![]() 4eg0C ![]() 4egjC ![]() 4ek2C ![]() 4eqyC ![]() 4ewgC ![]() 4exqC ![]() 4f2gC ![]() 4f32C ![]() 4f3nC ![]() 4f3yC ![]() 4f4hC ![]() 4f7dC ![]() 4fk8C ![]() 4fryC ![]() 4g1kC ![]() 4g67C ![]() 4ghkC ![]() 4h3yC ![]() 4h3zC ![]() 4h4gC ![]() 1qsgS S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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Components
#1: Protein | Mass: 28829.838 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: 1719B / Gene: fabI, BURPS1710b_2636 / Plasmid: BG1861 / Production host: ![]() ![]() References: UniProt: Q3JQY0, enoyl-[acyl-carrier-protein] reductase (NADH) #2: Chemical | ChemComp-CL / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.06 % |
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Crystal grow | Temperature: 298 K / pH: 7 Details: JCSG+ SCREEN: 10% PEG 6000, 100MM HEPES PH 7.0, VAPOR DIFFUSION, TEMPERATURE 298K, pH 7.00, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR 300 / Detector: CCD / Date: Aug 1, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→69.673 Å / Num. obs: 82541 / % possible obs: 95.5 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.142 / Rsym value: 0.142 / Net I/σ(I): 3.7 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.598 / Mean I/σ(I) obs: 1 / Rsym value: 0.598 / % possible all: 97.7 |
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Processing
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Refinement | Method to determine structure: ![]() ![]() Starting model: pdb entry 1qsg, tetramer, modified Resolution: 1.9→69.673 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.19 / SU ML: 0.092 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.54 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→69.673 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Number: 3021 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.9→1.95 Å / Total num. of bins used: 20
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